Assessment of Clostridium Difficile Genetic Relatedness

Supplemental Material

Table S1. Description of the 157 C. difficile study isolates.

Local ID / Culture
Date* / Source* / REA
Type / ST / MLVA Type / MLVA
CCa / CDR4b / CDR5 / CDR9 / CDR48 / CDR49 / CDR60 / tcdC
G129 / 2001 / REFLAB1 / AA 1 / 41 / 772 / E / null / null / 13 / 7 / 22 / 2 / A
G059 / 1989 / Minneapolis, MN / AA 1 / 41 / 708 / E / null / null / 14 / 8 / 20 / 2 / A
G111 / 1996 / REFLAB2 / AA 1 / 41 / 755 / E / null / null / 21 / 8 / 23 / 2 / A
G064 / 1989 / Minneapolis, MN / AA 1 / 41 / 712 / E / null / null / 19 / 8 / 24 / 2 / A
G076 / 1991 / Boston, MA / AA 2 / 41 / 725 / E / null / null / 14 / 9 / 24 / 2 / A
G130 / 2001 / REFLAB1 / AA 3 / 41 / 773 / E / null / null / 17 / 8 / 20 / 2 / A
G001 / 1982 / Minneapolis, MN / B 1 / 6 / 657 / B / 26 / 7 / 8 / 8 / 19 / 9 / 0
G006 / 1982 / Minneapolis, MN / B 1 / 6 / 662 / B / 19 / 7 / 8 / 8 / 19 / 9 / 0
G011 / 1982 / Minneapolis, MN / B 1 / 6 / 657 / B / 26 / 7 / 8 / 8 / 19 / 9 / 0
G013 / 1983 / Minneapolis, MN / B 1 / 6 / 657 / B / 26 / 7 / 8 / 8 / 19 / 9 / 0
G026 / 1984 / Minneapolis, MN / B 1 / 6 / 657 / B / 26 / 7 / 8 / 8 / 19 / 9 / 0
G031 / 1985 / Minneapolis, MN / B 1 / 6 / 683 / B / 25 / 7 / 8 / 8 / 20 / 10 / 0
G159 / 1985 / Minneapolis, MN / B 1 / 6 / 683 / B / 25 / 7 / 8 / 8 / 20 / 10 / 0
G039 / 1986 / Minneapolis, MN / B 1 / 6 / 688 / B / 26 / 7 / 8 / 8 / 20 / 9 / 0
G049 / 1987 / Minneapolis, MN / B 1 / 6 / 698 / B / 26 / 7 / 9 / 8 / 19 / 9 / 0
G053 / 1988 / Minneapolis, MN / B 1 / 6 / 702 / B / 16 / 7 / 8 / 8 / 20 / 10 / 0
G107 / 1996 / REFLAB2 / B 1 / 6 / 683 / B / 25 / 7 / 8 / 8 / 20 / 10 / 0
G002 / 1982 / Minneapolis, MN / B 2 / 6 / 658 / B / 21 / 7 / 8 / 8 / 17 / 9 / 0
G019 / 1982 / Minneapolis, MN / B 2 / 6 / 673 / B / 22 / 7 / 8 / 8 / 19 / 9 / 0
G055 / 1988 / Minneapolis, MN / B 2 / 6 / 704 / B / 29 / 7 / 8 / 8 / 19 / 9 / 0
G032 / 1985 / Minneapolis, MN / B 3 / 6 / 657 / B / 26 / 7 / 8 / 8 / 19 / 9 / 0
G048 / 1987 / Minneapolis, MN / B 3 / 6 / 697 / B / 26 / 7 / 8 / 8 / 10 / 9 / 0
G020 / 1982 / Minneapolis, MN / B 4 / 6 / 674 / B / 27 / 7 / 8 / 8 / 19 / 9 / 0
G036 / 1986 / Minneapolis, MN / B 5 / 6 / 688 / B / 26 / 7 / 8 / 8 / 20 / 9 / 0
G038 / 1986 / Minneapolis, MN / B 5 / 6 / 687 / B / 27 / 7 / 8 / 8 / 20 / 9 / 0
G022 / 1983 / Minneapolis, MN / B 7 / 6 / 674 / B / 27 / 7 / 8 / 8 / 19 / 9 / 0
G138 / 2003 / Portland, OR / BI 6 / 44 / 008 / D / 25 / 3 / 14 / 9 / 11 / 9 / 1
G139 / 2003 / Portland, OR / BI 6 / 44 / 008 / D / 25 / 3 / 14 / 9 / 11 / 9 / 1
G009 / 2004 / Chicago, IL / BI 6 / 44 / 665 / D / 20 / 3 / 14 / 10 / 19 / 10 / 1
G141 / 2004 / Chicago, IL / BI 6 / 44 / 665 / D / 20 / 3 / 14 / 10 / 19 / 10 / 1
G010 / 2004 / New Jersey / BI 6 / 44 / 666 / D / 19 / 3 / 13 / 9 / 14 / 10 / 1
G150 / 2004 / New Jersey / BI 6 / 44 / 787 / D / 18 / 3 / 13 / 9 / 12 / 10 / 1
G144 / 2005 / Pittsburgh, PA / BI 6 / 44 / 112 / D / 15 / 3 / 17 / 9 / 11 / 5 / 1
G023 / 2005 / Cleveland, OH / BI 6 / 44 / 536 / D / 16 / 3 / 15 / 9 / 12 / 8 / 1
G024 / 2005 / Cleveland, OH / BI 6 / 44 / 677 / D / 17 / 3 / 15 / 9 / 12 / 8 / 1
G151 / 2005 / Chicago, IL / BI 6 / 44 / 788 / D / 20 / 3 / 14 / 12 / 20 / 9 / 1
G062 / 1989 / Tucson,AZ / BK 1 / 41 / 711 / E / null / null / 10 / 9 / 13 / 2 / A
G142 / 2006 / REFLAB3,4 / BK 1 / 41 / 782 / E / null / null / 10 / 9 / 26 / 2 / A
G152 / 2006 / REFLAB3,4(porcine) / BK 1 / 41 / 789 / E / null / null / 11 / 8 / 26 / 2 / A
G100 / 1995 / Chicago,IL / BK 2 / 41 / 747 / E / null / null / 9 / 8 / 19 / 2 / A
G109 / 1996 / REFLAB2 / BK 3 / 41 / 660 / E / null / null / 10 / 6 / 15 / 2 / A
G004 / 2001 / Chicago,IL / BK 3 / 41 / 660 / E / null / null / 10 / 6 / 15 / 2 / A
G126 / 1999 / Chicago,IL / BK 4 / 41 / 769 / E / null / null / 13 / 11 / 20 / 2 / A
G146 / 2006 / REFLAB6 / BK 4 / 41 / 769 / E / null / null / 13 / 11 / 20 / 2 / A
G128 / 2003 / Chicago,IL / BK 5 / 41 / 771 / E / null / null / 9 / 9 / 16 / 2 / A
G148 / 2006 / REFLAB3,4 / BK 6 / 41 / 785 / E / null / null / 13 / 9 / 17 / 2 / A
G149 / 2006 / REFLAB3,4(porcine) / BK 6 / 41 / 786 / E / null / null / 11 / 9 / 17 / 2 / A
G153 / 2006 / REFLAB3,4(porcine) / BK 7 / 41 / 790 / E / null / null / 11 / 9 / 16 / 2 / A
G154 / 2006 / REFLAB3,4(porcine) / BK 8 / 41 / 644 / E / null / null / 12 / 8 / 25 / 2 / A
G043 / 2006 / REFLAB3,4 / BK 9 / 41 / 692 / E / null / null / 8 / 10 / 15 / 2 / A
G044 / 2006 / REFLAB3,4(bovine) / BK 10 / 41 / 693 / E / null / null / 11 / 8 / 23 / 2 / A
G080 / 2006 / REFLAB3,4(bovine) / BK 11 / 41 / 729 / E / null / null / 11 / 8 / 27 / 2 / A
G143 / 2006 / REFLAB3,4 / BK 12 / 41 / 783 / E / null / null / 10 / 9 / 24 / 2 / A
G018 / 2006 / REFLAB3,4(porcine) / BK 13 / 41 / 672 / E / null / null / 8 / 10 / 19 / 2 / A
G017 / 2006 / REFLAB3,4 / BK 14 / 41 / 671 / E / null / null / 13 / 8 / 29 / 2 / A
G108 / 1996 / REFLAB2 / CF 1 / 2 / 549 / F / 3 / Z40 / 33 / 8 / 16 / 7 / 7
G119 / 1998 / ATCC / CF 1 / 2 / 549 / F / 3 / Z40 / 33 / 8 / 16 / 7 / 7
G058 / 1988 / Minneapolis, MN / CF 1 / 2 / 707 / F / 3 / Z40 / 28 / 8 / 13 / 6 / 7
G068 / 1990 / Minneapolis, MN / CF 2 / 2 / 717 / F / 3 / Z40 / 26 / 6 / 7 / 6 / 7
G087 / 1993 / Minneapolis, MN / CF 2 / 2 / 550 / F / 3 / Z40 / 27 / 7 / 7 / 6 / 7
G003 / 2001 / Minneapolis, MN / CF 2 / 2 / 659 / F / 3 / Z40 / 28 / 7 / 10 / 7 / 7
G071 / 1990 / Minneapolis, MN / CF 3 / 2 / 720 / F / 3 / Z40 / 32 / 8 / 9 / 6 / 7
G116 / 1996 / Chicago, IL / CF 4 / 2 / 760 / F / 3 / Z40 / 34 / 7 / 8 / 6 / 7
G121 / 1999 / REFLAB2 / CF 4 / 2 / 764 / F / 3 / Z40 / 27 / 8 / 8 / 6 / 7
G123 / 1999 / REFLAB5 / CF 5 / 54 / 766 / F / 3 / Z40 / 36 / 8 / 13 / 8 / 7
G125 / 1999 / REFLAB5 / CF 6 / 2 / 768 / F / 3 / Z40 / 32 / 8 / 17 / 8 / 7
G127 / 1999 / Chicago, IL / CF 7 / 2 / 770 / F / 3 / Z40 / 23 / 6 / 9 / 7 / 7
G134 / 2003 / REFLAB6 / CF 11 / 2 / 776 / F / 3 / Z40 / 28 / 8 / 11 / 6 / 7
G135 / 2003 / REFLAB2 / CF 12 / 2 / 777 / F / 3 / Z40 / 29 / 8 / 7 / 8 / 7
G033 / 2003 / REFLAB7 / CF 14 / 2 / 684 / 12 / Z40 / 39 / 7 / 14 / 7 / 7
G034 / 2003 / REFLAB7 / CF 16 / 2 / 685 / F / 3 / Z40 / 31 / 8 / 8 / 6 / 7
G131 / 2000 / Chicago, IL / CF 17 / 53 / 774 / 27 / Z40 / 9 / 8 / 18 / 6 / null
G050 / 1988 / Minneapolis, MN / CG 1 / 52 / 699 / 33 / Z40 / 14 / 9 / 16 / 7 / 7
G122 / 1999 / REFLAB5 / CG 1 / 52 / 765 / 39 / Z40 / 6 / 9 / 19 / 6 / 7
G084 / 1991 / Boston, MA / CG 2 / 52 / 733 / 29 / Z40 / 18 / 13 / 14 / 7 / 7
G124 / 1999 / REFLAB5 / CG 3 / 52 / 767 / 33 / Z40 / 6 / 9 / 8 / 6 / 7
G012 / 1982 / Minneapolis, MN / G 1 / 9 / 667 / B / 24 / 7 / 6 / 6 / 15 / 2 / 0
G086 / 1992 / Minneapolis, MN / G 2 / 9 / 735 / 40 / 6 / 8 / 6 / 17 / 2 / 0
G027 / 1984 / Minneapolis, MN / G 4 / 55 / 679 / 28 / 2 / 5 / 13 / 13 / 8 / 21
G042 / 1987 / Minneapolis, MN / G 5 / 57 / 691 / 26 / 2 / 5 / 7 / 23 / 12 / 32
G063 / 1989 / Minneapolis, MN / G 6 / 48 / 713 / B / 17 / 8 / 6 / 4 / 11 / 2 / 0
G040 / 1986 / Minneapolis, MN / G 8 / 9 / 689 / B / 18 / 6 / 8 / 6 / 14 / 2 / 0
G105 / 1996 / REFLAB2 / G 9 / 9 / 752 / B / 17 / 7 / 7 / 8 / 20 / 2 / 0
G104 / 1994 / Chicago, IL / G 10 / 48 / 751 / 30 / 9 / 9 / 4 / 10 / 19 / 0
G156 / 1909 / Minneapolis, MN / G 12 / 9 / 792 / B / 29 / 6 / 8 / 6 / 16 / 2 / 0
G155 / 2006 / UNITED KINGDOM / J / 3 / 791 / A / 32 / 13 / 7 / 5 / 12 / 17 / 3
G037 / 1986 / Minneapolis, MN / J 1 / 3 / 547 / A / 37 / 16 / 6 / 6 / 13 / 19 / 3
G007 / 1982 / Minneapolis, MN / J 2 / 3 / 663 / A / 25 / 16 / 6 / 6 / 11 / 18 / 3
G074 / 1990 / Tucson, AZ / J 7 / 3 / 723 / A / 30 / 16 / 6 / 6 / 14 / 15 / 3
G081 / 1991 / Boston, MA / J 9 / 3 / 730 / A / 16 / 16 / 6 / 5 / 17 / 13 / 3
G157 / 1991 / Boston, MA / J 9 / 3 / 730 / A / 16 / 16 / 6 / 5 / 17 / 13 / 3
G091 / 1994 / Albany, NY / J 9 / 3 / 739 / A / 20 / 16 / 6 / 6 / 14 / 14 / 3
G092 / 1994 / Boston, MA / J 9 / 3 / 740 / A / 17 / 16 / 6 / 6 / 14 / 12 / 3
G095 / 1994 / REFLAB3,4 / J 9 / 3 / 742 / A / 20 / 16 / 6 / 6 / 14 / 15 / 3
G160 / 2005 / Chicago, IL / J 9 / 3 / 793 / A / 24 / 16 / 7 / 6 / 15 / 14 / 3
G085 / 1991 / Somerset, NJ / J 9 / 3 / 734 / A / 29 / 16 / 6 / 6 / 12 / 15 / 3
G133 / 2001 / Pittsburgh, PA / J 9 / 3 / 775 / A / 18 / 16 / 6 / 6 / 18 / 15 / 3
G115 / 1996 / Chicago, IL / J 9 / 3 / 759 / A / 28 / 16 / 7 / 6 / 14 / 15 / 3
G099 / 1995 / Chicago, IL / J 9 / 3 / 746 / A / 26 / 16 / 7 / 6 / 14 / 15 / 3
G145 / 2004 / Tucson, AZ / J 9 / 3 / 319 / A / 35 / 15 / 6 / 6 / 13 / 14 / 3
G061 / 1989 / Minneapolis, MN / J 13 / 3 / 710 / A / 34 / 16 / 6 / 6 / 14 / 17 / 3
G045 / 1987 / Minneapolis, MN / J 18 / 3 / 694 / A / 25 / 16 / 6 / 6 / 11 / 17 / 3
G114 / 1996 / REFLAB2 / J 27 / 3 / 758 / A / 23 / 13 / 7 / 5 / 10 / 17 / 3
G132 / 2001 / Pittsburgh, PA / J 28 / 3 / 24 / A / 23 / 16 / 6 / 6 / 15 / 15 / 3
G136 / 2006 / UNITED KINGDOM / J 33 / 3 / 778 / A / 34 / 14 / 7 / 5 / 9 / 18 / 3
G137 / 2006 / REFLAB6 / J 36 / 3 / 779 / 42 / 15 / 6 / 5 / 9 / 10 / 3
G073 / 1991 / Minneapolis, MN / K 1 / 6 / 722 / 35 / 8 / 10 / 6 / 21 / 9 / 0
G077 / 1991 / Boston, MA / K 2 / 6 / 726 / 50 / 8 / 10 / 6 / 19 / 9 / 0
G070 / 1990 / Minneapolis, MN / K 5 / 6 / 719 / C / 25 / 8 / 11 / 6 / 30 / 9 / 0
G097 / 1994 / Chicago, IL / K 12 / 6 / 744 / C / 26 / 8 / 11 / 6 / 31 / 9 / 0
G102 / 1995 / Chicago, IL / K 14 / 6 / 749 / C / 24 / 8 / 12 / 5 / 31 / 10 / 0
G120 / 1998 / Chicago, IL / K 18 / 6 / 763 / C / 29 / 8 / 11 / 6 / 30 / 9 / 0
G093 / 1995 / Boston, MA / K 20 / 6 / 741 / 38 / 8 / 10 / 5 / 19 / 9 / 0
G103 / 1995 / Chicago, IL / K 22 / 6 / 750 / 37 / 8 / 12 / 5 / 30 / 11 / 0
G117 / 1996 / Chicago, IL / K 27 / 6 / 761 / C / 27 / 8 / 11 / 6 / 32 / 9 / 0
G147 / 2005 / Washington,DC / K 29 / 6 / 784 / C / 25 / 8 / 11 / 6 / 29 / 9 / 0
G014 / 1983 / Minneapolis, MN / R 1 / 6 / 668 / A / 29 / 9 / 5 / 6 / 14 / 15 / 9
G052 / 1988 / Minneapolis, MN / R 3 / 6 / 701 / A / 26 / 10 / 5 / 6 / 15 / 16 / 9
G041 / 1986 / Minneapolis, MN / R 7 / 6 / 690 / A / 16 / 11 / 5 / 6 / 16 / 15 / 9
G016 / 1982 / Minneapolis, MN / R 9 / 6 / 670 / A / 20 / 10 / 5 / 6 / 15 / 15 / 9
G066 / 1990 / New York / R 11 / 5 / 715 / A / 31 / 9 / 5 / 6 / 13 / 15 / 9
G067 / 1990 / Minneapolis, MN / R 13 / 5 / 716 / A / 21 / 7 / 5 / 6 / 18 / 15 / 9
G083 / 1991 / Boston, MA / R 16 / 6 / 732 / A / 40 / 11 / 5 / 6 / 15 / 15 / 9
G079 / 1991 / Minneapolis, MN / R 19 / 6 / 728 / 23 / 5 / 6 / 6 / 13 / 14 / 9
G118 / 1998 / ARGENTINA / R 26 / 5 / 762 / A / 33 / 9 / 5 / 6 / 16 / 15 / 9
G112 / 1996 / REFLAB2 / R 29 / 6 / 756 / 51 / 11 / 5 / 6 / 17 / 16 / 9
G015 / 1983 / Minneapolis, MN / W 1 / 19 / 669 / B / 36 / 3 / 7 / 4 / 7 / 9 / 25
G140 / 2003 / Portland,OR / W 1 / 19 / 781 / 36 / 3 / 10 / 4 / 22 / 13 / 21
G090 / 1994 / Albany, NY / W 2 / 19 / 738 / 33 / 3 / 7 / 4 / 21 / 9 / 25
G110 / 1996 / REFLAB2 / W 3 / 19 / 754 / 31 / 3 / 7 / 5 / 17 / 11 / 21
G060 / 1989 / Minneapolis, MN / W 6 / 19 / 709 / B / 34 / 3 / 6 / 4 / 11 / 7 / 25
G094 / 1995 / Boston, MA / Y 1 / 1 / 17 / B / 33 / 6 / 10 / 4 / 11 / 3 / 9
G025 / 1983 / Minneapolis, MN / Y 1 / 1 / 678 / B / 33 / 6 / 6 / 5 / 13 / 4 / 9
G029 / 1985 / Minneapolis, MN / Y 1 / 1 / 681 / B / 25 / 6 / 11 / 5 / 15 / 3 / 9
G046 / 1987 / Minneapolis, MN / Y 1 / 1 / 695 / B / 15 / 4 / 10 / 5 / 10 / 3 / 9
G054 / 1988 / Minneapolis, MN / Y 1 / 1 / 703 / B / 37 / 6 / 10 / 5 / 20 / 4 / 9
G065 / 1990 / Minneapolis, MN / Y 1 / 1 / 714 / 32 / 6 / 9 / 5 / 5 / 3 / 9
G075 / 1991 / Boston, MA / Y 1 / 1 / 724 / 14 / 6 / 5 / 5 / 17 / 2 / 33
G089 / 1993 / Minneapolis, MN / Y 1 / 1 / 737 / B / 11 / 6 / 11 / 5 / 11 / 3 / 9
G096 / 1994 / Tucson, AZ / Y 1 / 1 / 743 / 52 / 6 / 9 / 5 / 9 / 3 / 9
G101 / 1995 / Chicago, IL / Y 1 / 1 / 748 / B / 19 / 6 / 10 / 5 / 13 / 3 / 9
G113 / 1996 / REFLAB2 / Y 8 / 1 / 757 / B / 21 / 6 / 6 / 5 / 11 / 3 / 9
G008 / 1982 / Minneapolis, MN / Y 12 / 36 / 664 / B / 21 / 6 / 8 / 4 / 21 / 10 / 9
G035 / 1986 / Minneapolis, MN / Y 15 / 1 / 686 / B / 27 / 6 / 7 / 6 / 15 / 4 / 9
G078 / 1991 / Tucson, AZ / Y 17 / 1 / 727 / B / 25 / 6 / 8 / 6 / 12 / 3 / 34
G072 / 1990 / Minneapolis, MN / Y 20 / 9 / 721 / B / 24 / 5 / 7 / 7 / 18 / 2 / 5
G051 / 1988 / Minneapolis, MN / Y 29 / 36 / 700 / B / 26 / 6 / 7 / 4 / 7 / 10 / 9
G098 / 1995 / Chicago, IL / Y 31 / 1 / 745 / B / 27 / 6 / 7 / 6 / 17 / 5 / 9
G021 / 1983 / Minneapolis, MN / Y 4 / 36 / 675 / 17 / 6 / 9 / 4 / 11 / 14 / 9
G028 / 1984 / Minneapolis, MN / Y 4 / 49 / 680 / B / 17 / 6 / 11 / 7 / 16 / 8 / 9
G030 / 1985 / Minneapolis, MN / Y 4 / 36 / 682 / B / 23 / 6 / 8 / 4 / 4 / 13 / 9
G047 / 1987 / Minneapolis, MN / Y 4 / 36 / 696 / 41 / 6 / 7 / 4 / 9 / 11 / 9
G057 / 1988 / Minneapolis, MN / Y 4 / 36 / 706 / B / 20 / 6 / 9 / 4 / 23 / 16 / 9
G069 / 1990 / Minneapolis, MN / Y 4 / 49 / 718 / 33 / 7 / 7 / 7 / 8 / 6 / 9
G082 / 1991 / Boston, MA / Y 4 / 49 / 731 / B / 27 / 6 / 7 / 7 / 17 / 8 / 9
G088 / 1993 / Minneapolis, MN / Y 4 / 36 / 736 / 38 / 6 / 8 / 4 / 15 / 14 / 9
G106 / 1996 / REFLAB2 / Y 4 / 49 / 753 / B / 18 / 6 / 11 / 7 / 17 / 7 / 9

aMLVA clonal complex (CC) defined by types with 6 isolate and STRD 10 (Figure 2, A-F);bNull, did not amplify.Shaded rows represent the REA types with multiple isolates used to assess MLVA stability over time.

*The city and/or state or country and year of culture are listed for each isolate when this information was available. If the isolates were sent to the Hines VA Hospital (HVA)C. difficile Research Laboratory from another laboratory, the source is referred to as REFLABand the year it was received at the HVA laboratory are listed instead. REFLAB isolates included submissions from the following institutions (and the lead investigators):1University of Maribor, Maribor, Slovenia (M. Rupnik); 2 Anaerobe Reference Laboratory, NPHS for Wales, Cardiff, UK (J. Brazier); 3Centers for Disease Control, Atlanta, GA (L.C. McDonald); 4University of Arizona, Tucson, AZ (G. Songer); 5Univerisité Catholilque de Louvain, Brussels, Belgium (M. Delmee); 6Leiden University Medical Center, Leiden, The Netherlands (E.J. Kuijper); 7National Institute of Infectious Diseases, Tokyo, Japan (H. Kato).

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